= Implementation of the analysis step =

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<div class="wiki-toc">
<h4>Implementation Guide</h4>
<ol><li><a href="ImplementationGuide">Main page</a></li>
<li><a href="AdaptParallelization">Adaptation of the parallelization</a></li>
<li><a href="InitPdaf">Initialization of PDAF</a></li>
<li><a href="ModifyModelforEnsembleIntegration">Modifications for ensemble integration</a></li>
<li>Implementation of the analysis step</li>
<ol>
<li><a href="ImplementAnalysisseik">Implementation for SEIK</a></li>
<li><a href="ImplementAnalysislseik">Implementation for LSEIK</a></li>
</ol>
<li><a href="AddingMemoryandTimingInformation">Memory and timing information</a></li>
</ol>
</div>
}}}

The implementation of the analysis step requires that the user-supplied routines whose names are given in the call to the filter-specific put-state routine are implemented with full functionality. 

Several of the routines are general and hence usable for all filter algorithms. There are some differences between local (LSEIK and LETKF) and global filters (SEIK, SEEK, EnKF, ETKF). The routines are described in separate pages for each filter algorithm. The general routines will be pedeated, but they are marked to be general.

Filter-specific implementations:
 * [ImplementAnalysisseik Implementation of the analysis for SEIK]
 * [ImplementAnalysislseik Implementation of the analysis for LSEIK]

== Testing the full implementation ==

After the implementation of the user-supplied routines for the analysis step, the data assimilation system is fully implemented. In order to test the program one has to compile it without setting 'PDAF_NO_UPDATE'. 

To speed up the testing it can be useful to comment out the time stepping part. In that case only the model initialization and the assimilation cycle would be executed, without the usually costly time integration of the ensemble. One should then check if all user-supplied routines perform as they should.